AMATH/BIOL 382 Problem Set 1 Due January 22, 2010
1. Notes, chapter 1: Exercise 1.1.11. 2. Consider the chemical reaction network indicated in Figure 1 with rate constants as shown.
k1 k3
E F
A B
k2
C D
Figure 1: Closed Network a) Write a set of six diere
AMATH/BIOL 382 Problem Set 1 Solutions
1. One can begin by observing that equation two factors as 0 = 2ass (2 bss ). The case ass = 0 can be ruled out, since this cannot satisfy the rst equation. Thus bss = 2. Substituting into the rst equation gives 0 =
Chemistry 350 Assignment 5: Solutions December 5th 2005 Question 1
Q19.2
For a reaction mechanism to be considered correct, what property must it demonstrate? In order to be valid, a proposed reaction mechanism must agree with the experimentally determine
Session 07
Data Analysis in Mathcad Topics
In this session the following spreadsheet concepts will be explored: 1. Statistical Functions in Mathcad 2. Error Bars 3. Interpolation Linear Interpolation Cubic Spline Interpolation 4. Curve Fitting Simple Line
Session 08
Solving Equations in Mathcad Topics
In this session the following spreadsheet concepts will be explored: 1. Iterative Solutions The root() function The polyroots() function 2. Solving Simultaneous Linear Equations Solving Linear Equations by Ma
Session 06
Algebra and Calculus in Mathcad Topics
In this session the following spreadsheet concepts will be explored: 1. A Review of Linear Algebra Determinants Matrices 2. Working with Matrices in Mathcad C Defining a Matrix C Modifying Matrices C Matri
Session 10
Exchanging Data Topics
In this session the following spreadsheet concepts will be explored: 1. Sharing Data Between Mathcad and Excel Copying and Pasting. Mathcad Data Table 2. Importing Data from Other Applications Importing into a Mathcad Dat
Session 05
An Introduction to Mathcad - The Electronic Scratchpad Topics
In this session the following spreadsheet concepts will be explored: 1. What is Mathcad? 2. Mathcad Basics The Mathcad Workspace Order of Evaluation Equal Signs Functions Entering Eq
Session 03
Data Analysis in Excel Topics
In this session the following spreadsheet concepts will be explored: 1. Basic Statistics in Science Distributions Mean Variance and Standard Deviation Method of Least Squares 2. Basic Statistical Functions in Excel
CHEM350 (Winter 2010) Statistical Mechanics and Kinetics Final exam information TIME: Wednesday, April 14, 12:30-15:00 LOCATION: PAC 9 Final Exam is based on all the material covered this term. A Summary is given below. References are to: Engel and Reid,
Session 09
Symbolic Math in Mathcad Topics
In this session the following spreadsheet concepts will be explored: 1. Using Symbolic Math 2. Manipulating Equations Expand Factor Substitute Simplify Collect Partial-Fraction Expansion Float 3. Symbolic Matrix
Biology 365
Databases and additional information
available through NCBI
(Ch. 2 of Pevsner)
Lecture03
>gi|32698832|ref|NP_872303.1|MTSDCSSTHCSPESCGTASGCAPASSCSVETACLP
SequencedatabasesinNCBI
Sources of information:
http:/www.ncbi.nlm.nih.gov
PubMedInformat
Biology 365
Introduction to Sequence Alignments
Lecture04
Importance of Sequence Alignments
Sequence alignment is the most fundamental tool of
bioinformatics
used to determine if two sequences are
evolutionarily related (homologous)
also which regions
Biology 365
Databases and exploring NCBI
Objectives:
- Gain an understanding of the key components of bioinformatics
databases
- Accessing and retrieving data from the U.S. National Center for
Biotechnology Information (NCBI)
Lecture2
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Biol 365:
An introduction to BLAST
Lecture07
Database searching
Sequence alone is not informative
- want to deduce function
BLAST is a set of algorithms to compare a query
sequence against all sequences in database
Similarity is measured by aligning tw
Biology 365
Basic Local Alignment Search
Tool (BLAST), continued.
(Pevsner, Ch. 4)
Objective:
To examine the algorithms and statistics used by
BLAST
Lecture09
The BLAST algorithm
Covered so far:
BLAST is a heuristic local alignment search tool
runs fast
Biology 365
Methods of Pairwise
Sequence Alignment
(Pevsner Ch. 3)
Objective:
To examine
algorithms for the
alignment of two
sequences
Lecture05
Scores (nucleotides)
In a gap free alignment, score is determined by the
amount of aligned pairs of identical
Biology 365
Scoring matrices
(Pevsner, Ch. 3)
Objective:
To examine the theory behind amino acid scoring
matrices
Lecture07
General approach to pairwise alignment
Choose two sequences
Select an algorithm that generates a score
Allow gaps (insertions, d
Session 01
Introduction to Excel - Spreadsheet Basics Topics
In this session the following spreadsheet concepts will be explored: 1. What is a Spreadsheet? 2. Understanding the Worksheet Excel keyboard shortcuts 3. Entering Data on a Worksheet Entering te
Tutorial 2
A Mathcad Tutorial
In this exercise, you will create a worksheet that calculates simple algebraic functions (such as x2, x3, and x2 + x3).
Entering Data
With Mathcad, there are many ways in which we can enter data. In this exercise, we wish to
Chemistry 350 Midterm Solutions November 1, 2004 1. (20 marks) Briey answer each of the following: (a) Sketch, on one set of axes, the compressibility Z if a gas vs. pressure P for an ideal gas, for a slightly non-ideal gas, and for a very non-ideal gas.
CHEM 350 Lectures 11 and 12, January 27 and 29, 2010 Ensemble Averages.
variable v : having M possible values v1 , v2 , , vM : corresponding probabilities p1 , p2 , , pM N systems in ensemble with variable v having value vr in Nr = N pr of them with so m
CHEM 350 Lecture 10, January 25, 2010 Fluctuations (continued)
The number of atoms on a given side varies from frame to frame though not by much these are local uctuations which occur even though our system is in equilibrium For a small number of particle
CHEM 350 Lecture 7, 8, and 9, January 18, 20, and 22, 2010 Introduction to Statistical Mechanics. There are two general approaches to the description of physical systems: i) Macroscopic: large units of matter; units mol, mmol, etc. mechanical variables: V
CHEM 350 Lecture 6, January 15, 2010 Relation between B2 (T ) and intermolecular interactions. We shall consider only the simplest case: that of a gas of lledshell [or 1 S state] atoms, such as He, Ne, Ar. If V (R) is the potential energy (energy of inter
1/1 CHEM350: Lecture 5, Jan 13 2010 Gibbs free energy for nonideal gases (section 7.5 in textbook) (continued) Notice that G o (T ) in the previous expression is the ideal gas pressure at 1 bar. This means that the standard state of the nonideal gas is 1